We have developed a method which uses a series of discriminant analyses to allocate a protein sequence of unknown function to one of a number of functional groups (toxins, immunoglobulin variable regions, cytochromes c, etc.). Allocation is based on characteristics of both global and local physical properties (hydrophobicity, charge, etc.) of the amino acid sequence, and also on the appearance in the sequence of some characteristics petterns, such as repeated consecutive appearance of certain residues, or short signature peptides.